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Yorodumi- PDB-1rrv: X-ray crystal structure of TDP-vancosaminyltransferase GtfD as a ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rrv | |||||||||
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Title | X-ray crystal structure of TDP-vancosaminyltransferase GtfD as a complex with TDP and the natural substrate, desvancosaminyl vancomycin. | |||||||||
Components |
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Keywords | TRANSFERASE/ANTIBIOTIC / GT-B / GLYCOSYLTRANSFERASE / ROSSMANN FOLD / GLYCOPEPTIDE / VACOSAMYCIN / ANTIBIOTIC / TRANSFERASE-ANTIBIOTIC COMPLEX | |||||||||
Function / homology | Function and homology information devancosaminyl-vancomycin vancosaminetransferase / vancomycin biosynthetic process / hexosyltransferase activity / lipid glycosylation / carbohydrate metabolic process Similarity search - Function | |||||||||
Biological species | AMYCOLATOPSIS ORIENTALIS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Mulichak, A.M. / Lu, W. / Losey, H.C. / Walsh, C.T. / Garavito, R.M. | |||||||||
Citation | Journal: Biochemistry / Year: 2004 Title: Crystal Structure of Vancosaminyltransferase Gtfd from the Vancomycin Biosynthetic Pathway: Interactions with Acceptor and Nucleotide Ligands Authors: Mulichak, A.M. / Lu, W. / Losey, H.C. / Walsh, C.T. / Garavito, R.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rrv.cif.gz | 177.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rrv.ent.gz | 137.9 KB | Display | PDB format |
PDBx/mmJSON format | 1rrv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rr/1rrv ftp://data.pdbj.org/pub/pdb/validation_reports/rr/1rrv | HTTPS FTP |
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-Related structure data
Related structure data | 1pn3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | Biological assembly is a monomer. |
-Components
-Protein / Protein/peptide / Sugars , 3 types, 6 molecules ABCD
#1: Protein | Mass: 43905.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) AMYCOLATOPSIS ORIENTALIS (bacteria) / Gene: GTFD / Plasmid: PET22B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9AFC7 #2: Protein/peptide | Type: Glycopeptide / Class: Antibiotic / Mass: 1149.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: DESVANCOSAMINYL VANCOMYCIN IS AN INTERMIDIATE IN VANCOMYCIN BIOSYNTHESIS. IT IS TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY D-GLUCOSE (RESIDUE 8) ON RESIDUE 4. Source: (natural) AMYCOLATOPSIS ORIENTALIS (bacteria) / References: NOR: NOR00681, DESVANCOSAMINYL VANCOMYCIN #6: Sugar | Type: D-saccharide, beta linking, Glycopeptide / Class: Antibiotic / Mass: 180.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Formula: C6H12O6 Details: DESVANCOSAMINYL VANCOMYCIN IS AN INTERMIDIATE IN VANCOMYCIN BIOSYNTHESIS. IT IS TRICYCLIC GLYCOPEPTIDE, GLYCOSYLATED BY D-GLUCOSE (RESIDUE 8) ON RESIDUE 4. References: DESVANCOSAMINYL VANCOMYCIN |
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-Non-polymers , 4 types, 507 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Compound details | VANCOMYCIN DESVANCOSAMINYL IS A TRICYCLIC GLYCOPEPTIDE, A MEMBER OF THE VANCOMYCIN FAMILY. THE ...VANCOMYCIN |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.79 % |
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Crystal grow | pH: 7 Details: NA,K PHOSPHATE, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 17, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→30 Å / Num. obs: 66022 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rsym value: 0.074 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.96→2.04 Å / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PN3 Resolution: 2→30 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 37.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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